Examples of Samples

The following examples show how to enter samples for specific use cases.

Using Individually Addressable Lanes with Projects

• Use the Individually Addressable Lanes add-on with two library pools and associate samples with projects Library_Pool_1 or Library_Pool_2.

[Samples],,,
SampleName,Index1,Index2,Lane,Project
Sample_1,CCC,AAA,1,Library_Pool_1
Sample_2,TTT,GGG,1,Library_Pool_1
Sample_3,AAA,GGG,2,Library_Pool_2

Adding Custom Metadata

• Add a custom column, Custom_Metadata, with metadata Sample_1_metadata, Sample_2_metadata, and Sample_3_metadata.

[Samples],,,
SampleName,Index1,Index2,Lane,Custom_Metadata
Sample_1,CCC,,1,Sample_1_metadata
Sample_2,TTT,,1,Sample_2_metadata
Sample_3,AAA,,1,Sample_3_metadata

Defining Index Sequences

• Associate a sample named ID1 with the Index 1 sequences AAAA and TTTT. You can organize the index sequences within a single column and use a plus sign (+) to combine them. You can also list the index sequences in individual sample rows.

[Samples]
SampleName,Index1
ID1,AAAA+TTTT

[Samples]
SampleName,Index1
ID1,AAAA
ID1,TTTT

• Associate a sample named ID1 to a combined Index 1 and Index 2 sequence, AAAATTTT.

[Samples]
SampleName,Index1,Index2
ID1,AAAA,TTTT

• Associate a sample named ID1 to the combined Index 1 and Index 2 sequences AAAATTTT and CCCCGGGG.

[Samples]
SampleName,Index1,Index2
ID1,AAAA,TTTT
ID1,CCCC,GGGG

• Associate a sample named ID1 to the combined Index 1 and Index 2 sequences AAAATTTT, AAAAGGGG, CCCCTTTT, and CCCCGGGG.

[Samples]
SampleName,Index1,Index2
ID1,AAAA+CCCC,TTTT+GGGG

Reconciling Different Index Sequence Lengths

If the index sequences for samples in a run manifest do not have the same length, use one of the following approaches to reconcile the difference:

• Use a single run manifest and append the first nucleotides of the adapter read next in sequencing to the end of shorter index sequences. This addition allows the shorter index sequences to match the length of the longest index sequence.

• Use two run manifests with different index sequence lengths, and execute Bases2Fastq twice. Make sure to update any impacted settings, such as base masks.

The following examples demonstrate these approaches for a scenario with two samples with different index sequence lengths. Sample1 uses 8 bp index sequences and Sample2 uses 10 bp index sequences. The run manifest contains sequences for R1Adapter and R2Adapter, and the sequencing run uses the outer primer 5' AGATCGGAAGAGCACACGTCTGAACTCCAGTCA 3'.

[Settings]
R1Adapter, CGTGCTGGATTGGCTCACCAGACACCTTCCGACAT
R2Adapter, AGTTGACAAGCGGTAGCCTGCACACCTTCCGACAT
[Samples]
SampleName,Index1,Index2
Sample1,AGGCAGAA,TGCTACGA
Sample2,CGTTCTCTTG,CACCAAGTGG

Use a Single Run Manifest

To use a single run manifest for this scenario, revise the run manifest index sequences as follows:

1. Append the first two nucleotides of the outer primer (AG) to the end of the Index1 sequence for Sample1.
2. Append the first two nucleotides of the R1Adapter (CG) to the end of the Index2 sequence for Sample1.

[Settings]
R1Adapter, CGTGCTGGATTGGCTCACCAGACACCTTCCGACAT
R2Adapter, AGTTGACAAGCGGTAGCCTGCACACCTTCCGACAT
[Samples]
SampleName,Index1,Index2
Sample1,AGGCAGAAAG,TGCTACGACG
Sample2,CGTTCTCTTG,CACCAAGTGG

Use Two Run Manifests

The following example run manifests show the same samples and index sequences in two run manifests.

• Run Manifest A contains the 8 bp index sequences for Sample1.
• Run Manifest B contains the 10 bp index sequences for Sample2.

Run Manifest A, Sample 1 (8 bp)

[Settings]
R1Adapter, CGTGCTGGATTGGCTCACCAGACACCTTCCGACAT
R2Adapter, AGTTGACAAGCGGTAGCCTGCACACCTTCCGACAT
I1Mask, I1:Y8N*
I2Mask, I2:Y8N*
[Samples]
SampleName,Index1,Index2
Sample1,AGGCAGAA,TGCTACGA

Run Manifest B, Sample 2 (10 bp)

[Settings]
R1Adapter, CGTGCTGGATTGGCTCACCAGACACCTTCCGACAT
R2Adapter, AGTTGACAAGCGGTAGCCTGCACACCTTCCGACAT
I1Mask, I1:Y10N*
I2Mask, I2:Y10N*
[Samples]
SampleName,Index1,Index2
Sample2,CGTTCTCTTG,CACCAAGTGG